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1ky9

Crystal Structure of DegP (HtrA)

Method: X-RAY DIFFRACTION Dmax: 115.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEASE DO

Escherichia coli

UniProt P0C0V0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 27–474 Mutation：S210A Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.275
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain B； UniProt 27–474 Mutation：S210A Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Isopropanol, PEG 2000 MME, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K Resolution 2.80 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1KY9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2ZLE Cryo-EM structure of DegP12/OMP Deposited 2008-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 27–474（448 aa）
Chain B 27–474（448 aa）
Chain C 27–474（448 aa）
Chain E 27–474（448 aa）
Chain F 27–474（448 aa）
Chain G 27–474（448 aa）
Chain H 27–474（448 aa）
Chain I 27–474（448 aa）
Chain J 27–474（448 aa）
Chain K 27–474（448 aa）
Chain L 27–474（448 aa）
Chain M 27–474（448 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE；Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity
Resolution 28.00 Å
3CS0 Crystal structure of DegP24 Deposited 2008-04-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain A 27–474（448 aa）
Mutation：S210A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, vapor diffusion, temperature 292K
Resolution 3.00 Å R-free 0.274
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 27–474（448 aa）
Mutation：S210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 3.10 Å R-free 0.309
3MH4 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain B 27–474（448 aa）
Mutation：S210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 3.10 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 27–474（448 aa）
Not recorded DFP DIISOPROPYL PHOSPHONATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 3.00 Å R-free 0.309
3MH5 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain B 27–474（448 aa）
Not recorded DFP DIISOPROPYL PHOSPHONATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 3.00 Å R-free 0.309
3MH6 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 27–474（448 aa）
Not recorded DFP DIISOPROPYL PHOSPHONATE × 24 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；12% Isopropanol, 0.1M Tris, 12% PEG 2000 MME, pH 8.5, VAPOR DIFFUSION, temperature 293K
Resolution 3.60 Å R-free 0.309
3MH7 HtrA proteases are activated by a conserved mechanism that can be triggered by distinct molecular cues Deposited 2010-04-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric
Chain A 27–474（448 aa）
Mutation：S210A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；PEG 550 MME, NaCl, pH 8.5, VAPOR DIFFUSION, temperature 292K
Resolution 2.96 Å R-free 0.249
3OTP Crystal structure of the DegP dodecamer with a model substrate Deposited 2010-09-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 27–474（448 aa） Fragment：UNP residues 27-474
Chain B 27–474（448 aa） Fragment：UNP residues 27-474
Chain C 27–474（448 aa） Fragment：UNP residues 27-474
Chain D 27–474（448 aa） Fragment：UNP residues 27-474
Chain E 27–474（448 aa） Fragment：UNP residues 27-474
Chain F 27–474（448 aa） Fragment：UNP residues 27-474
Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.6；291 K；65 mM citric acid, 35 mM Bis-Tris propane, 8% PEG3350, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K
Resolution 3.76 Å R-free 0.251
3OU0 re-refined 3CS0 Deposited 2010-09-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 27–474（448 aa） Fragment：DegP, UNP residues 27-474
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.229
4A8D DegP dodecamer with bound OMP Deposited 2011-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 27–474（448 aa） Fragment：DEGP
Chain B 27–474（448 aa） Fragment：DEGP
Chain C 27–474（448 aa） Fragment：DEGP
Chain D 27–474（448 aa） Fragment：DEGP
Chain E 27–474（448 aa） Fragment：DEGP
Chain F 27–474（448 aa） Fragment：DEGP
Chain G 27–474（448 aa） Fragment：DEGP
Chain H 27–474（448 aa） Fragment：DEGP
Chain I 27–474（448 aa） Fragment：DEGP
Chain J 27–474（448 aa） Fragment：DEGP
Chain K 27–474（448 aa） Fragment：DEGP
Chain L 27–474（448 aa） Fragment：DEGP
Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 300MM NACL, 50MM HEPES- NAOH；pH 8；300MM NACL, 50MM HEPES- NAOH
cryo-EM vitrification conditions Cryogen ETHANE；EMBEDDED IN VITREOUS ICE USING C-FLAT HOLEY CARBON GRIDS AND A VITROBOT AT 20C.
Resolution 28.00 Å
6JJK Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 35–474（440 aa）
Chain B 35–474（440 aa）
Chain C 35–474（440 aa）
Chain D 35–474（440 aa）
Chain E 35–474（440 aa）
Chain F 35–474（440 aa）
Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；10% PEG3350 and 0.1 M tacsimate pH 3.4
Resolution 3.60 Å R-free 0.265
6JJL Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 35–474（440 aa）
Chain B 35–474（440 aa）
Chain C 35–474（440 aa）
Chain D 35–474（440 aa）
Chain E 35–474（440 aa）
Chain F 35–474（440 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350, 0.1 M tacsimate pH 3.5
Resolution 4.20 Å R-free 0.326
6JJO Crystal structure of the DegP dodecamer with a modulator Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 27–474（448 aa）
Chain B 27–474（448 aa）
Chain C 27–474（448 aa）
Chain D 27–474（448 aa）
Chain E 27–474（448 aa）
Chain F 27–474（448 aa）
Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A Mutation：S210A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；11% PEG3350 and 0.1 M tacsimate pH 3.5
Resolution 4.16 Å R-free 0.278
8F0A Client-bound structure of a DegP trimer within a 12mer cage Deposited 2022-11-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.60 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F0U Structure of a 12mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 54 PDB declaration: 54-meric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1T Structure of an 18mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 12.10 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 72 PDB declaration: 72-meric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F1U Structure of a 24mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 13.80 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 90 PDB declaration: 90-meric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F21 Structure of a 30mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain B 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain C 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain E 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Chain F 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 14.10 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 180 PDB declaration: 180-meric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å
8F26 Structure of a 60mer DegP cage bound to the client protein hTRF1 Deposited 2022-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–385（348 aa） Fragment：protease and PDZ1 domains (UNP residues 38-385)
Chain D 400–474（75 aa） Fragment：PDZ2 domain (UNP residues 400-474)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 9.70 Å

18 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DEGP_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–448； UniProt 27–474 Author chain B； PDBConstruct 1–448； UniProt 27–474

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1ky9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ky9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ky9
Deposition date deposition_date2002-02-04
Structure title titleCrystal Structure of DegP (HtrA)
Keywords keywords;protein quality control, serine protease, trypsin, chaperone, PDZ, ATP-independent, temperature-regulated, periplasm, cage-forming protein, HYDROLASE ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.11 Å
Radius of gyration Rg (electron density) rg_electron32.71 Å
Forward intensity I(0) i096342900.00
Molecular weight molecular_weight75420.0 kDa
Excluded volume excluded_volume93343 ų
Envelope volume envelope_volume133850 ų
Hydration-shell volume shell_volume34810 ų
Envelope diameter envelope_diameter121.7 Å
Shell Rg shell_rg38.36 Å
Envelope Rg envelope_rg33.07 Å
Shape Rg shape_rg32.72 Å
Total Rg total_rg33.17 Å
Total atoms total_atoms5200
Residues n_residues682
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.4 Å
Rg (real space) rg_real33.21 Å
Rg uncertainty (real space) rg_real_error0.98 Å
I(0) (real space) i0_real9.6340e+07
I(0) uncertainty (real space) i0_real_error1.8190e+06
Rg (reciprocal space) rg_reciprocal33.17 Å
I(0) (reciprocal space) i0_reciprocal96340000.0000
Solution quality estimate total_estimate0.8758
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.9 Å
Skewness Skewness skewness0.369
Kurtosis Kurtosis kurtosis-0.332
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha14610000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1ky9a1
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.4 — HtrA-like serine proteases
Domain ID domain_idd1ky9a2
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.1 — Prokaryotic proteases
Domain ID domain_idd1ky9b1
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.4 — HtrA-like serine proteases
Domain ID domain_idd1ky9b2
Class classb — All beta proteins
Fold Fold foldb.36 — PDZ domain-like
Superfamily Superfamily superfamilyb.36.1 — PDZ domain-like
Family Family familyb.36.1.4 — HtrA-like serine proteases
Domain ID domain_idd1ky9b3
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.1 — Prokaryotic proteases

CATH v4.4 (7 domains)

Domain ID domain_id1ky9A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ky9A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ky9A03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id1ky9B01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ky9B02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1ky9B03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
Domain ID domain_id1ky9B04
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain
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8. Citations (1)

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9. Files and Curves (10)